diff main.py @ 4:84f685c067ad draft default tip

"planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"

--- a/main.py	Mon Jul 19 13:11:45 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,623 +0,0 @@
-___author___ = "Richard Hohensinner"
-___created___ = "04.02.2021"
-___last_modified___ = "20.05.2021"
-
-# general imports
-import os, sys, json
-
-from shutil import copyfile
-from datetime import datetime
-
-# irods-client imports
-from irods.session import iRODSSession
-from irods.models import Collection, DataObject
-from irods.query import SpecificQuery
-
-# Tkinter imports
-from tkinter import messagebox, Label, Button, Entry, Listbox, Tk, PhotoImage, Grid
-
-# global variables
-session = None
-file_path_list = []
-selected_file = ""
-session_success = False
-selection_success = False
-iRODSCredentials = {"host": "", "port": "", "user": "", "pw": "", "zone": ""}
-python_path = []
-
-
-########################################################################################################################
-#   Main function of the iRODS tools
-#
-#   IN:
-#   JSON Object params (argv[1])
-#   OUT:
-#
-########################################################################################################################
-def main():
-
-    # check input parameters
-    if len(sys.argv) == 2:
-        params = json.loads(sys.argv[1])
-    else:
-        raise Exception("Invalid Parameters submitted!")
-
-    tool_type = params["tool_type"]
-
-    try:
-        if params["tool_type"] != "up" and params["tool_type"] != "down":
-            raise Exception("Invalid tool-type parameter submitted!")
-    except:
-        raise Exception("No tool-type parameter submitted!")
-    is_download_call = True
-    if tool_type == "up":
-        is_download_call = False
-
-    # check params for integrity
-    result_string, params_faulty = check_params(params)
-
-    if params_faulty:
-        raise Exception(result_string)
-
-    global iRODSCredentials, session_success, selected_file, selection_success
-    iRODSCredentials["host"] = params["irods_host"]
-    iRODSCredentials["port"] = params["irods_port"]
-    iRODSCredentials["zone"] = params["irods_zone"]
-
-    # create login window
-    ## make_login_window(params)
-    iRODSCredentials["user"] = params["irods_user"]
-    iRODSCredentials["pw"] = params["irods_password"]
-    
-    host = iRODSCredentials["host"]
-    port = iRODSCredentials["port"]
-    user = iRODSCredentials["user"]
-    password = iRODSCredentials["pw"]
-    zone = iRODSCredentials["zone"]
-
-    iRODSsession = get_iRODS_connection(host=host, port=port, user=user, password=password, zone=zone)
-    global session, session_success
-    try:
-        coll = iRODSsession.collections.get("/" + zone + "/" + "home" + "/" + user)
-    except Exception:
-        raise Exception("Invalid Login")
-
-    if coll:
-        session = iRODSsession
-        session_success = True
-    
-    
-    # check tool settings and start tool execution
-    if session_success:
-        # initialize download tool
-        if params["tool_type"] == "down":
-
-            selected_file = params["file_path"]
-            params["user"] = iRODSCredentials["pw"]
-            params["password"] = iRODSCredentials["user"]
-            # start download routine
-            handle_download_call(params)
-
-        # initialize upload tool
-        elif params["tool_type"] == "up":
-
-            if session_success:
-                params["user"] = iRODSCredentials["pw"]
-                params["password"] = iRODSCredentials["user"]
-                # start upload routine
-                handle_upload_call(params)
-            else:
-                raise Exception("Logging into iRODS failed")
-    else:
-        raise Exception("Logging into iRODS failed")
-# -------------------------------------------------------------------------------------------------------------------- #
-
-
-########################################################################################################################
-#   Login Window class for Tkinter
-#
-#   IN:
-#   Tk Window win
-#   OUT:
-#   (sets global variables iRODSCredentials, session and session_success)
-#
-########################################################################################################################
-class LoginWindow:
-    def __init__(self, win):
-        self.window = win
-        self.lbl1 = Label(win, text='iRODS Username:')
-        self.lbl2 = Label(win, text='iRODS Password:')
-        self.t1 = Entry(bd=3)
-        self.t2 = Entry(show="*")
-        self.b1 = Button(win, text='Login', command=self.login)
-
-        self.window.grid()
-        Grid.rowconfigure(self.window, 0, weight=1)
-        Grid.rowconfigure(self.window, 1, weight=1)
-        Grid.rowconfigure(self.window, 2, weight=1)
-        Grid.rowconfigure(self.window, 3, weight=1)
-        Grid.rowconfigure(self.window, 4, weight=1)
-        Grid.columnconfigure(self.window, 0, weight=1)
-
-        self.lbl1.grid(row=0, column=0, padx="20", pady="1", sticky="w")
-        self.t1.grid(row=1, column=0, padx="10", pady="1", sticky="nsew")
-        self.lbl2.grid(row=2, column=0, padx="20", pady="1", sticky="w")
-        self.t2.grid(row=3, column=0, padx="10", pady="1", sticky="nsew")
-        self.b1.grid(row=4, column=0, padx="50", pady="10", sticky="nsew")
-
-    def login(self):
-        global iRODSCredentials
-        user = str(self.t1.get())
-        password = str(self.t2.get())
-        if user == "" or password == "":
-            self.window.iconify()
-            messagebox.showerror("Error", "Username or Password empty!")
-            self.window.deiconify()
-            return
-        else:
-            iRODSCredentials["user"] = user
-            iRODSCredentials["pw"] = password
-
-        get_irods_session(self.window)
-        if not session_success:
-            return
-
-        self.window.destroy()
-# -------------------------------------------------------------------------------------------------------------------- #
-
-
-########################################################################################################################
-#   File Selection Window class for Tkinter
-#
-#   IN:
-#   Tk Window win
-#   OUT:
-#   (sets global variables selected_file and selection_success)
-#
-########################################################################################################################
-class FileSelectWindow:
-    def __init__(self, win):
-        global session, iRODSCredentials
-        self.session = session
-        self.window = win
-        self.b1 = Button(win, text='Select', command=self.select)
-        self.lb1 = Listbox(win)
-
-        self.window.grid()
-        Grid.rowconfigure(self.window, 0, weight=1)
-        Grid.rowconfigure(self.window, 1, weight=1)
-        Grid.columnconfigure(self.window, 0, weight=1)
-
-        self.lb1.grid(row=0, column=0, padx="20", pady="1", sticky="nswe")
-        self.b1.grid(row=1, column=0, padx="50", pady="1", sticky="ew")
-
-        coll = session.collections.get("/" + iRODSCredentials["zone"] + "/" + "home" + "/" + iRODSCredentials["user"])
-        file_list = []
-
-        self.get_files_from_collections(coll, file_list)
-
-        for counter in range(len(file_list)):
-            self.lb1.insert(counter, file_list[counter])
-
-    def get_files_from_collections(self, coll, file_list):
-        for obj in coll.data_objects:
-            file_list.append(obj.path)
-
-        for col in coll.subcollections:
-            self.get_files_from_collections(col, file_list)
-
-    def select(self):
-        global session, selected_file, selection_success
-        try:
-            selection = self.lb1.get(self.lb1.curselection())
-        except:
-            self.window.iconify()
-            messagebox.showerror("Error", "No file selected!")
-            self.window.deiconify()
-            return
-
-        selected_file = selection
-        selection_success = True
-        self.window.destroy()
-# -------------------------------------------------------------------------------------------------------------------- #
-
-
-########################################################################################################################
-#   Creates an iRODS session and sets the global session variable
-#
-#   IN:
-#   Tk Window window
-#
-#   OUT:
-#
-########################################################################################################################
-def get_irods_session(window):
-    global iRODSCredentials
-    host = iRODSCredentials["host"]
-    port = iRODSCredentials["port"]
-    user = iRODSCredentials["user"]
-    password = iRODSCredentials["pw"]
-    zone = iRODSCredentials["zone"]
-
-    iRODSsession = get_iRODS_connection(host=host, port=port, user=user, password=password, zone=zone)
-    global session, session_success
-    try:
-        coll = iRODSsession.collections.get("/" + zone + "/" + "home" + "/" + user)
-    except Exception:
-        window.iconify()
-        messagebox.showerror("Error", "Invalid Authentification")
-        window.deiconify()
-        return
-
-    if coll:
-        session = iRODSsession
-        session_success = True
-# -------------------------------------------------------------------------------------------------------------------- #
-
-
-########################################################################################################################
-#   Helper function to initialize Login Window classes and Tk windows
-#
-#   IN:
-#
-#   OUT:
-#
-########################################################################################################################
-def make_login_window(params):
-    #get login icon
-    log_img = ""
-    for dirpath, dirnames, filenames in os.walk(params["galaxy_root"]):
-        for fn in filenames:
-            if fn == "irods_galaxy_login.png":
-                log_img = os.path.join(dirpath, fn)
-            if log_img != "":
-                break
-        if log_img != "":
-            break
-    # print(log_img)
-    
-    window = Tk()
-    LoginWindow(window)
-    window.title('iRODS Login')
-    window.geometry("450x225+10+10")
-    window.minsize(450, 225)
-    window.tk.call('wm', 'iconphoto', window._w, PhotoImage(file=log_img))
-    # alternative options:
-    # window.iconphoto(False, PhotoImage(file='/path/to/ico/icon.png'))
-    # window.iconbitmap("/home/richard/git/galaxy_irods_tools/login.ico")
-    window.mainloop()
-# -------------------------------------------------------------------------------------------------------------------- #
-
-
-########################################################################################################################
-#   Helper function to initialize File Selection Window classes and Tk windows
-#
-#   IN:
-#
-#   OUT:
-#
-########################################################################################################################
-def make_file_select_window():
-    window = Tk()
-    FileSelectWindow(window)
-    window.title('iRODS File Select')
-    window.geometry("450x225+10+10")
-    window.minsize(450, 225)
-    window.mainloop()
-# -------------------------------------------------------------------------------------------------------------------- #
-
-
-########################################################################################################################
-#   Checks whether arguments are valid and returns true/false depending on params
-#
-#   IN:
-#   Dict params
-#
-#   OUT:
-#   String res_string
-#   Bool res_bool
-########################################################################################################################
-def check_params(params):
-    res_string = ""
-    res_bool = False
-
-    try:
-        if params["irods_host"] == "":
-            res_string += "Host empty!\n"
-            res_bool = True
-        if params["irods_port"] == "":
-            res_string += "Port empty!\n"
-            res_bool = True
-        if params["irods_zone"] == "":
-            res_string += "Zone empty!\n"
-            res_bool = True
-        ##if params["selection_type"] == "path" and params["file_path"] == "":
-        ##    res_string += "Missing file path!\n"
-        ##    res_bool = True
-    except:
-        raise Exception("Invalid/Missing Parameters")
-
-    return res_string, res_bool
-# -------------------------------------------------------------------------------------------------------------------- #
-
-
-########################################################################################################################
-#   Function to handle iRODS download calls
-#
-#   IN:
-#   Dict params
-#
-#   OUT:
-#
-########################################################################################################################
-def handle_download_call(params):
-
-    global session, selected_file
-
-    # check if /ZONE/USER/...FILE... pattern is valid
-    if len(selected_file.split("/")) < 2:
-        raise Exception("Path to file is not valid in iRODS")
-
-    file_list = []
-
-    # check if file is a directory
-    if "." not in selected_file:
-        try:
-            coll = session.collections.get(selected_file)
-            for file in coll.data_objects:
-                file_list.append(file.path)
-        except:
-            raise Exception("Invalid directory path specified!")
-    else:
-        file_list.append(selected_file)
-
-    # get registry file
-    reg_file = ""
-    for dirpath, dirnames, filenames in os.walk(params["galaxy_root"]):
-        for fn in filenames:
-            if fn == "irods_galaxy_registry.xml":
-                reg_file = os.path.join(dirpath, fn)
-            if reg_file != "":
-                break
-        if reg_file != "":
-            break
-
-    # print(file_list)
-    # print(os.getcwd())
-
-    # handle download for all files in file_list
-    for f in file_list:
-
-        file_to_get = f
-
-        # handle path and file name
-        name_file_to_get = file_to_get.split("/")[-1]
-        path_file_to_get = "/".join(file_to_get.split("/")[0:len(file_to_get.split("/")) - 1])
-
-        # check iRODS filesystem
-        check_iRODS_destination(session, path_file_to_get, name_file_to_get)
-
-        # get file object from iRODS
-        iRODS_file_object = session.data_objects.get(path_file_to_get + "/" + name_file_to_get)
-        input_file = iRODS_file_object.open("r+")
-        output_file = open(name_file_to_get, "wb")
-        output_file.write(input_file.read())
-        #input_file.seek(0,0)
-        #print(input_file.read().decode("utf-8"))
-        #temp = open("/home/richard/test.txt", "w")
-        #input_file.seek(0,0)
-        #temp.write(input_file.read().decode("utf-8"))
-	
-        input_file.close()
-        output_file.close()
-
-        abs_file_path = os.path.abspath(name_file_to_get)
-
-        file_type = str(name_file_to_get.split(".")[-1])
-
-        file_content = {"uuid": None,
-                        "file_type": "auto",
-                        "space_to_tab": False,
-                        "dbkey": "?",
-                        "to_posix_lines": True,
-                        "ext": file_type,
-                        "path": abs_file_path,
-                        "in_place": True,
-                        "dataset_id": params["job_id"],
-                        "type": "file",
-                        "is_binary": False,
-                        "link_data_only": "copy_files",
-                        "name": name_file_to_get
-                        }
-
-        with open("temporal.json", "w") as fileParams:
-            fileParams.write(json.dumps(file_content))
-        fileParams.close()
-
-        # load file into Galaxy by using the integrated upload tool - Preparation
-        python_command = params["galaxy_root"] + "/tools/data_source/upload.py"
-        arg1 = params["galaxy_root"]
-        arg2 = params["galaxy_datatypes"]
-        arg3 = os.path.abspath(fileParams.name)
-        arg4 = params["job_id"] + ":" + params["out_dir"] + ":" + params["out_file"]
-        arg5 = params["galaxy_root"] + "/lib/galaxy"
-
-        # copy sample registry.xml to working directory
-        copyfile(reg_file, params["galaxy_datatypes"])
-
-        # activate environment for new process call and call the python upload command either both with
-        #sys.path.append(params["galaxy_root"] + "/lib")
-        #os.system("python -c \'import sys;sys.path.append(\"" + params["galaxy_root"] + "/lib\")\'" + "&& python3 " +
-        #          python_command + " " + arg1 + " " + arg2 + " " + arg3 + " " + arg4)
-        
-        # get upload file
-        upload_file = ""
-        for dirpath, dirnames, filenames in os.walk(params["galaxy_root"]):
-            for fn in filenames:
-                if fn == "irods_upload.py":
-                    upload_file = os.path.join(dirpath, fn)
-                if upload_file != "":
-                    break
-            if upload_file != "":
-                break
-                
-        global python_path
-        python_path = sys.path
-        os.system(params["galaxy_root"] + "/.venv/bin/python " +  upload_file + " " + arg1 + " " + arg2 + " " + arg3 + " " + arg4)
-    # close connection
-    session.cleanup()
-# -------------------------------------------------------------------------------------------------------------------- #
-
-
-########################################################################################################################
-#   Function to handle iRODS upload calls
-#
-#   IN:
-#   Dict params
-#
-#   OUT:
-#
-########################################################################################################################
-def handle_upload_call(params):
-
-    global session, iRODSCredentials
-
-    path_to_file = params["up_file_path"]
-    name_of_file = params["up_file"]
-    #print(path_to_file)
-    #print(name_of_file)
-
-    coll_path = "/" + iRODSCredentials["zone"] + "/home/" + iRODSCredentials["user"] + "/galaxyupload"
-    try:
-        coll = session.collections.get(coll_path)
-    except:
-        coll = session.collections.create(coll_path)
-
-    now = datetime.now()
-
-    # dd/mm/YY
-    day = now.strftime("%d%m%Y")
-    time = now.strftime("%H%M%S")
-
-    coll_path = coll_path + "/" + day
-
-    try:
-        coll = session.collections.get(coll_path)
-    except:
-        coll = session.collections.create(coll_path)
-    
-    if "/" in name_of_file:
-        name_of_file = name_of_file.split("/")[-1]
-    
-    irods_file_name = time + "_" + name_of_file
-    iRODS_file_object = session.data_objects.create(coll_path + "/" + irods_file_name)
-    iRODS_file_object = session.data_objects.get(coll_path + "/" + irods_file_name)
-
-    irods_file = iRODS_file_object.open("w")
-    galaxy_file = open(path_to_file, "rb")
-    content = galaxy_file.read()
-    irods_file.write(content)
-
-    print("Successfully uploaded: " + name_of_file + "\n as: " + irods_file_name)
-    # TODO can't close session without writing process finished - but reading/writing happens async.
-    # session.cleanup()
-
-    pass
-# -------------------------------------------------------------------------------------------------------------------- #
-
-
-########################################################################################################################
-#   Function to initialize an iRODS Session - will raise an Exception if timeout is longer than 2 seconds
-#
-#   IN:
-#   String host
-#   String port
-#   String user
-#   String password
-#   String zone
-#
-#   OUT:
-#   iRODSSession-object session
-########################################################################################################################
-def get_iRODS_connection(host, port, user, password, zone):
-
-    # initialize timeout checker - fires after 2 secs
-    import signal
-    signal.signal(signal.SIGALRM, timeout_checker)
-    signal.alarm(2)
-
-    try:
-        session = iRODSSession(host=host, port=port, user=user, password=password, zone=zone)
-    except Exception:
-        raise Exception("There was a timeout creating the iRODS session")
-
-    # void/reset alarm
-    signal.alarm(0)
-
-    return session
-# -------------------------------------------------------------------------------------------------------------------- #
-
-
-########################################################################################################################
-#   Helper function to raise timeout exception when SIGALRM fires
-#
-#   IN:
-#
-#   OUT:
-#
-########################################################################################################################
-def timeout_checker():
-
-    raise Exception("iRODS session timeout")
-# -------------------------------------------------------------------------------------------------------------------- #
-
-
-########################################################################################################################
-#   Function to check if file exists in iRODS
-#
-#   IN:
-#   String path
-#
-#   OUT:
-#   Bool ret_bool
-#
-########################################################################################################################
-def check_if_file_exists(path):
-
-    if os.path.isfile(path):
-        ret_bool = True
-    else:
-        ret_bool = False
-
-    return ret_bool
-# -------------------------------------------------------------------------------------------------------------------- #
-
-
-########################################################################################################################
-#   Function to check iRODS destination
-#
-#   IN:
-#   iRODSSession-object session
-#   String path
-#   String name
-#
-#   OUT:
-#   Bool ret_bool
-#
-########################################################################################################################
-def check_iRODS_destination(session, path, name):
-
-    try:
-        session.collections.get(path.rstrip("/"))
-    except Exception:
-        raise Exception("Collection doesn't exist in iRODS file system")
-
-    try:
-        session.data_objects.get(path.rstrip("/") + "/" + name)
-    except Exception:
-        raise Exception("File doesn't exist in iRODS file system")
-# -------------------------------------------------------------------------------------------------------------------- #
-
-
-if __name__ == "__main__":
-    main()